Selective and Enriched Dependency Figures
Neekesh Dharia & Guillaume Kugener
2020-08-18
Generated using: 20Q1
The table below highlights all of the cell lines that are included in the analyses and the types that they are annotated as:
Overview
- Evaluate selective dependencies across adult and pediatric cell lines by comparing rates of dependency
- Identify selective dependencies that occur more frequently in pediatric cell lines
- Calculate enriched dependencies and plot across pediatric tumor types
Dependency example densities
Selective dependency rates
Bar plots
All selective dependencies
<2% Adult, >3% Peds
Rate difference p<0.05
Both >5%
Tables
Genes with p.adj < 0.05 for fraction of peds > adult.
Genes with p.adj < 0.05 for fraction of adult > peds.
Genes with pediatric LRT dep rate - adults LRT dep rate > 5%.
Genes with adult LRT dep rate - peds LRT dep rate > 5%.
Genes with adult LRT dep rate >2% and pediatric >2%.
Genes with pediatric LRT dep rate >4% and double adults LRT dep rate.
Genes with adult LRT dep rate >5% and pediatric >5%.
Genes with adult LRT dep rate >0% or pediatric >0%.
Genes with adult LRT dep rate >0% and pediatric >0%.
Genes with pediatric LRT dep rate >2%.
Genes with adult LRT dep rate >2%.
Circle plots
Heatmap of selective dependencies in at least 3 pediatric cell lines
Enriched dependencies
Number of cell lines in tumor type vs number of enriched dependencies
All enriched dependencies
Enriched selective dependencies
Enriched dependencies by tumor type plots
Peds only, highlight selective deps
Highlight transcription factors
Session Info
devtools::session_info()## ─ Session info ───────────────────────────────────────────────────────────────
## setting value
## version R version 3.6.2 (2019-12-12)
## os macOS Catalina 10.15.6
## system x86_64, darwin15.6.0
## ui X11
## language (EN)
## collate en_US.UTF-8
## ctype en_US.UTF-8
## tz America/New_York
## date 2020-08-18
##
## ─ Packages ───────────────────────────────────────────────────────────────────
## package * version date lib source
## AnnotationDbi 1.48.0 2019-10-29 [1] Bioconductor
## ape 5.3 2019-03-17 [1] CRAN (R 3.6.0)
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## bibtex 0.4.2.2 2020-01-02 [1] CRAN (R 3.6.0)
## Biobase 2.46.0 2019-10-29 [1] Bioconductor
## BiocGenerics 0.32.0 2019-10-29 [1] Bioconductor
## BiocManager 1.30.10 2019-11-16 [1] CRAN (R 3.6.0)
## BiocParallel 1.20.1 2019-12-21 [1] Bioconductor
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## caTools 1.18.0 2020-01-17 [1] CRAN (R 3.6.0)
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## dplyr * 0.8.5 2020-03-07 [1] CRAN (R 3.6.0)
## DT * 0.13 2020-03-23 [1] CRAN (R 3.6.0)
## ellipsis 0.3.0 2019-09-20 [1] CRAN (R 3.6.0)
## enrichplot 1.6.1 2019-12-16 [1] Bioconductor
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## lmtest 0.9-37 2019-04-30 [1] CRAN (R 3.6.0)
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## magrittr * 1.5 2014-11-22 [1] CRAN (R 3.6.0)
## MASS 7.3-51.5 2019-12-20 [1] CRAN (R 3.6.0)
## Matrix 1.2-18 2019-11-27 [1] CRAN (R 3.6.2)
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## multtest 2.42.0 2019-10-29 [1] Bioconductor
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## plotrix 3.7-7 2019-12-05 [1] CRAN (R 3.6.0)
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##
## [1] /Library/Frameworks/R.framework/Versions/3.6/Resources/library